These projects are in a usable form. Packages have been developed following
RECON’s standards, are fully functional, documented and tested, and have been
released on CRAN.
Discretized probability distributions.
Quantifying transmissibility throughout an epidemic from incidence time series.
Estimation of infectiousness in the early stage of an outbreak
Handling, visualisation and analysis of epidemiological contacts.
Small helpers and tricks for epidemics analysis
Computation, handling, visualisation and simple modelling of incidence.
Convert dates to arbitrary week definitions including epiweek, isoweek, and more
Modular framework for outbreak reconstruction.
Collection of outbreak data.
Projections of future incidence
Open training platform for epidemics analysis
Visualisation and analysis of passenger flows
The RECON packages listed below are still in development. They may be functional
already, but a stable version has yet to be released.
Analysis of transmission chains using branching processes.
R Estimation from Cluster Sizes
Rationalised and reproducible data cleaning.
Install devel versions of RECON packages by default.
Portable environment for epidemics analysis
Investigation of food-borne disease outbreaks.
Docker images for RECON packages
Graphical user interface for epicontacts
Helpers and wrappers for mapping diseases
Finding matching patient records across tabular data sets.
Tutorials and code gists for mapping infectious diseases
Graphical user interface for incidence
Tools to Import and Tidy Case Linelist Data
Pack up R to take away
Tools to develop RECON packages
Template shiny GUI for RECON packages
Facilitate rmarkdown workflows
Visualisation and Monitoring of Epidemics, including some outbreak detection algorithms.
The packages listed below mostly predate RECON, but have been authored by RECON
members and are relevant for infectious disease epidemiology.
Basic analysis and visualisation of complex line-list data (to be replaced by incidence and epicontacts).
Implementation of a generic json format for case outbreak data.
R package implementing EpiJSON format.
Inferring transmission chains using temporal and genetic information.
Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
Dynamical Systems Approach to Infectious Disease Epidemiology - a Shiny/R based teaching tool.
Mathematical Modeling of Infectious Disease Dynamics
Molecular clock dating of pathogen phylogenies.
Phylodynamic inference of effective population size through time.